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      Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons

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          Abstract

          Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000–10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons.

          Abstract

          Serial crystallography was developed for protein crystal data collection with X-ray free-electron lasers. Here the authors present several examples which show that serial crystallography using high-viscosity injectors can also be routinely employed for room-temperature data collection at synchrotrons.

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          Most cited references49

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          Linking crystallographic model and data quality.

          In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R(merge) values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R(merge) values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.
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            Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.

            Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.
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              Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.

              Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.
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                Author and article information

                Contributors
                joerg.standfuss@psi.ch
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                14 September 2017
                14 September 2017
                2017
                : 8
                : 542
                Affiliations
                [1 ]ISNI 0000 0001 1090 7501, GRID grid.5991.4, Laboratory of Biomolecular Research, Division of Biology and Chemistry, , Paul Scherrer Institut, ; 5232 Villigen PSI, Switzerland
                [2 ]LeadXpro AG, Park InnovAARE, 5234 Villigen PSI, Switzerland
                [3 ]ISNI 0000 0001 1018 9466, GRID grid.419494.5, Molecular Membrane Biology, , Max-Planck Institute of Biophysics, ; Max-von-Laue-Straße 3, 60438 Frankfurt, Germany
                [4 ]ISNI 0000 0001 1090 7501, GRID grid.5991.4, Science IT, , Paul Scherrer Institut, ; 5232 Villigen PSI, Switzerland
                [5 ]ISNI 0000 0001 1090 7501, GRID grid.5991.4, SwissFEL, , Paul Scherrer Institut, ; 5232 Villigen PSI, Switzerland
                [6 ]ISNI 0000 0001 1090 7501, GRID grid.5991.4, Macromolecular Crystallography, , Swiss Light Source, Paul Scherrer Institut, ; 5232 Villigen PSI, Switzerland
                [7 ]GRID grid.451116.6, Heptares Therapeutics Ltd, ; Biopark Broadwater Road, Welwyn Garden City, AL7 3AX UK
                [8 ]ISNI 0000 0001 0725 7771, GRID grid.445003.6, Linac Coherent Light Source, , SLAC National Accelerator Laboratory, ; 2575 Sand Hill Road, Menlo Park, CA 94025 USA
                [9 ]ISNI 0000 0001 2156 2780, GRID grid.5801.c, Department of Biology, , ETH Zurich, ; 8093 Zürich, Switzerland
                [10 ]ISNI 0000 0004 1937 0642, GRID grid.6612.3, University of Basel, ; Biozentrum, Basel 4056 Switzerland
                Author information
                http://orcid.org/0000-0002-8040-7753
                Article
                630
                10.1038/s41467-017-00630-4
                5599499
                28912485
                3131eccd-b8a8-4db5-be95-776fdab28a6a
                © The Author(s) 2017

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 30 March 2017
                : 14 July 2017
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